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Old 07-15-2012, 05:30 PM   #1
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Location: St. Louis

Join Date: Jul 2012
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Default error querying custom database using Blast+

So I am trying to query stomach ETS libraries for my gene of interest. I installed blast ncbi-blast-2.2.26+.dmg on mac OSX lion. I downloaded an ETS library as a .seq file which I converted to a .fsa file and made it into a blast database using makeblastdb which gave me the following files;


These files are in /Users/jgeahlen/NCBI_Blast/db, which is a different directory than the blast files since my computer installed it in a directory I don't have permission to modify via command line.

When I try to blast that database using the script below;

Jessicas-MacBook-Air:db jgeahlen$ blastn -db TSTOM2 -query /Users/jgeahlen/NCBI_Blast/input/human3.fsa -out TSTOM2.out

I get the following error; BLAST Database error: No alias or index file found for nucleotide database [TSTOM2] in search path [/Users/jgeahlen/NCBI_Blast/db::/Users/jgeahlen/NCBI_Blast/db:]

but when I look in /Users/jgeahlen/NCBI_Blast/db, there they are

I have created a .ncbirc file and designated BLASTDB=/Users/jgeahlen/NCBI_Blast/db

Both my query and database were made from nucleotide sequences so that cannot be the issue. Please help!

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Old 07-16-2012, 03:27 AM   #2
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You specified a database name TSTOM2 so BLAST is looking for an index file named TSTOM2.nin (or an alias file named TSTOM2.nal). Your BLAST database name is TSTOM2.fsa. Change your command to '-db TSTOM2.fsa'.
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Old 07-16-2012, 09:26 AM   #3
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That seems to have solved the problem, thanks!!!
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Old 12-29-2012, 10:48 AM   #4
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Last edited by sfyoung; 12-29-2012 at 11:55 AM. Reason: Deleting to start new thread
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